79 research outputs found
Using the local density approximation and the LYP, BLYP, and B3LYP functionals within Reference--State One--Particle Density--Matrix Theory
For closed-shell systems, the local density approximation (LDA) and the LYP,
BLYP, and B3LYP functionals are shown to be compatible with reference-state
one-particle density-matrix theory, where this recently introduced formalism is
based on Brueckner-orbital theory and an energy functional that includes exact
exchange and a non-universal correlation-energy functional. The method is
demonstrated to reduce to a density functional theory when the
exchange-correlation energy-functional has a simplified form, i.e., its
integrand contains only the coordinates of two electron, say r1 and r2, and it
has a Dirac delta function -- delta(r1 - r2) -- as a factor. Since Brueckner
and Hartree--Fock orbitals are often very similar, any local exchange
functional that works well with Hartree--Fock theory is a reasonable
approximation with reference-state one-particle density-matrix theory. The LDA
approximation is also a reasonable approximation. However, the Colle--Salvetti
correlation-energy functional, and the LYP variant, are not ideal for the
method, since these are universal functionals. Nevertheless, they appear to
provide reasonable approximations. The B3LYP functional is derived using a
linear combination of two functionals: One is the BLYP functional; the other
uses exact exchange and a correlation-energy functional from the LDA.Comment: 26 Pages, 0 figures, RevTeX 4, Submitted to Mol. Phy
Random-phase approximation and its applications in computational chemistry and materials science
The random-phase approximation (RPA) as an approach for computing the
electronic correlation energy is reviewed. After a brief account of its basic
concept and historical development, the paper is devoted to the theoretical
formulations of RPA, and its applications to realistic systems. With several
illustrating applications, we discuss the implications of RPA for computational
chemistry and materials science. The computational cost of RPA is also
addressed which is critical for its widespread use in future applications. In
addition, current correction schemes going beyond RPA and directions of further
development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012
Regulation of MicroRNA Biogenesis: A miRiad of mechanisms
microRNAs are small, non-coding RNAs that influence diverse biological functions through the repression of target genes during normal development and pathological responses. Widespread use of microRNA arrays to profile microRNA expression has indicated that the levels of many microRNAs are altered during development and disease. These findings have prompted a great deal of investigation into the mechanism and function of microRNA-mediated repression. However, the mechanisms which govern the regulation of microRNA biogenesis and activity are just beginning to be uncovered. Following transcription, mature microRNA are generated through a series of coordinated processing events mediated by large protein complexes. It is increasingly clear that microRNA biogenesis does not proceed in a 'one-size-fits-all' manner. Rather, individual classes of microRNAs are differentially regulated through the association of regulatory factors with the core microRNA biogenesis machinery. Here, we review the regulation of microRNA biogenesis and activity, with particular focus on mechanisms of post-transcriptional control. Further understanding of the regulation of microRNA biogenesis and activity will undoubtedly provide important insights into normal development as well as pathological conditions such as cardiovascular disease and cancer
Quasi-periodic acceleration of electrons by a plasmoid-driven shock in the solar atmosphere
Cosmic rays and solar energetic particles may be accelerated to relativistic
energies by shock waves in astrophysical plasmas. On the Sun,
shocks and particle acceleration are often associated with the eruption
of magnetized plasmoids, called coronal mass ejections (CMEs).
However, the physical relationship between CMEs and shock particle
acceleration is not well understood. Here, we use extreme ultraviolet,
radio and white-light imaging of a solar eruptive event on 22 September
2011 to show that a CME-induced shock (Alfvén Mach number 2:4+0:7
-0:8) was coincident with a coronal wave and an intense metric radio burst
generated by intermittent acceleration of electrons to kinetic energies
of 2{46 keV (0.1{0.4 c). Our observations show that plasmoid-driven
quasi-perpendicular shocks are capable of producing quasi-periodic acceleration
of electrons, an effect consistent with a turbulent or rippled
plasma shock surface
The VHL-dependent regulation of microRNAs in renal cancer
Extent: 17p.Background
The commonest histological type of renal cancer, clear cell renal cell carcinoma (cc RCC), is associated with genetic and epigenetic changes in the von Hippel-Lindau (VHL) tumour suppressor. VHL inactivation leads to induction of hypoxia-inducible factors (HIFs) and a hypoxic pattern of gene expression. Differential levels of specific microRNAs (miRNAs) are observed in several tumours when compared to normal tissue. Given the central role of VHL in renal cancer formation, we examined the VHL-dependent regulation of miRNAs in renal cancer.
Methods
VHL-dependent miRNA expression in cc RCC was determined by microarray analysis of renal cell line RCC4 with mutated VHL (RCC4-VHL) and reintroduced wild-type VHL (RCC4 + VHL). Five miRNAs highly upregulated in RCC4 + VHL and five miRNAs highly downregulated in RCC4 + VHL were studied further, in addition to miR-210, which is regulated by the HIF-VHL system. miRNA expression was also measured in 31 cc RCC tumours compared to adjacent normal tissue.
Results
A significant increase in miR-210, miR-155 and miR-21 expression was observed in the tumour tissue. miR-210 levels also showed a correlation with a HIF-regulated mRNA, carbonic anhydrase IX (CAIX), and with VHL mutation or promoter methylation. An inverse correlation was observed between miR-210 expression and patient survival, and a putative target of miR-210, iron-sulfur cluster assembly protein (ISCU1/2), shows reciprocal levels of mRNA expression in the tumours.
Conclusions
We have identified VHL-regulated miRNAs and found that for some the regulation is HIF-dependent and for others it is HIF-independent. This pattern of regulation was also seen in renal cancer tissue for several of these miRNAs (miR-210, miR-155, let-7i and members of the miR-17-92 cluster) when compared with normal tissue. miR-210 showed marked increases in expression in renal cancer and levels correlated with patient survival. The inverse correlation between miR-210 levels and ISCU1/2 provides support for the hypothesis that ISCU1/2 is a target of miR-210 and that it may contribute to the anaerobic respiration seen in renal (and other) tumours.Calida S Neal, Michael Z Michael, Lesley H Rawlings, Mark B Van der Hoek and Jonathan M Gleadl
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